The geometries, polarizabilities (αs), and first hyperpolarizabilities (βtot) of a series of green fluorescent protein chromophore coupled diradicals and their corresponding optical isomers were investigated using density functional theory (DFT). The results show that the introductions of the electron donor/acceptor significantly enhance the polarizabilities and have a different influence on the first hyperpolarizabilities. For trans isomers, the βtot values of the studied compounds increase with increasing strength of the electron-withdrawing ability of the substituent, whereas the βtot values decrease significantly with increasing strength of the electron-donating ability of the substituent. For cis isomers, the trends in the changes in the βtot values are the opposite of those for trans isomers on introduction of a donor/acceptor. Significantly, photoisomerization can lead to the different βtot values. The βtot values of cis isomers are smaller than those of trans isomers when electron acceptors are introduced. For example, the βtot value of the cis isomer with the strongest electron acceptor, i.e., ―NO2, is about 1/6 that of the corresponding trans isomer. However, the βtot values of trans isomers are smaller than those of cis isomers when electron donors are introduced. For example, the βtot value of the trans isomer with the strongest electron donor, i.e., ―NH2, is about six times smaller than that of the corresponding cis isomer. As a result, photoisomerization can modulate the molecular nonlinear optical (NLO) responses effectively.